.Dd Oct 10, 2019
.Os "Open Babel" 3.1
.Dt obminimize 1 URM
.Sh NAME
.Nm obminimize
.Nd "optimize the geometry, minimize the energy for a molecule"
.Sh SYNOPSIS
.Nm
.Op Ar OPTIONS
.Ar filename
.Sh DESCRIPTION
The
.Nm
tool can be used to minimize the energy for molecules
inside (multi-)molecule files (e.g., MOL2, etc.)
.Sh OPTIONS
If no filename is given,
.Nm
will give all options including the available forcefields.
.Bl -tag -width flag
.It Fl c Ar criteria
Set convergence criteria (default=1e-6)
.It Fl cg
Use conjugate gradients algorithm (default)
.It Fl sd
Use steepest descent algorithm
.It Fl newton
Use Newton2Num linesearch (default=Simple)
.It Fl ff Ar forcefield
Select the forcefield
.It Fl o Ar format
Select the output file format
.It Fl h
Add hydrogen atoms
.It Fl n Ar steps
Specify the maximum numer of steps (default=2500)
.It Fl cut
Use cut-off (default=don't use cut-off)
.It Fl rvdw Ar rvdw
Specify the VDW cut-off distance (default=6.0)
.It Fl rele Ar rele
Specify the Electrostatic cut-off distance (default=10.0)
.It Fl pf Ar freq
Specify the frequency to update the non-bonded pairs (default=10)
.El
.Sh EXAMPLES
.Pp
View the possible options, including available forcefields:
.Dl "obminimize"
.Pp
Minimize the energy for the molecule(s) in file test.mol2:
.Dl "obminimize test.mol2"
.Pp
Minimize the energy for the molecule(s) in file test.mol2 using the
Ghemical forcefield:
.Dl "obminimize -ff Ghemical test.mol2"
.Pp
Minimize the energy for the molecule(s) in file test.mol2 by taking
at most 300 geometry optimization steps
.Dl "obminimize -n 300 test.mol2"
.Pp
Minimize the energy for the molecule(s) in file test.mol2 using the
steepest descent algorithm and convergence criteria 1e-5:
.Dl "obminimize -sd -c 1e-5 test.mol2"
.Sh SEE ALSO
.Xr obabel 1 ,
.Xr obenergy 1 ,
.Xr obrotamer 1 .
.Pp
The web pages for Open Babel can be found at:
\%<\fBhttp://openbabel.org/\fR>
.Pp
The web pages for Open Babel Molecular Mechanics can be found at:
\%<\fBhttp://openbabel.org/wiki/Molecular_mechanics\fR>
.Sh AUTHORS
The minimize program was contributed by
.An Tim Vandermeersch.
.Pp
.An -nosplit
Open Babel is developed by a cast of many, including current maintainers
.An Geoff Hutchison ,
.An Chris Morley ,
.An Michael Banck ,
and innumerable others who have contributed fixes and additions.
For more contributors to Open Babel, see
\%<\fBhttp://openbabel.org/wiki/THANKS\fR>
.Sh COPYRIGHT
Copyright (C) 2007 by Tim Vandermeersch.
.Pp
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
.Pp
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
